[med-svn] [Git][med-team/hyphy][master] 6 commits: debian/rules: set LC_ALL to fix groff warnings in the manpages
Michael R. Crusoe
gitlab at salsa.debian.org
Sat Feb 20 10:35:55 GMT 2021
Michael R. Crusoe pushed to branch master at Debian Med / hyphy
Commits:
d5618e5a by Michael R. Crusoe at 2021-02-20T10:57:50+01:00
debian/rules: set LC_ALL to fix groff warnings in the manpages
- - - - -
0f6f9b96 by Michael R. Crusoe at 2021-02-20T11:05:30+01:00
debian/patches/spelling: fix some typos
- - - - -
4e3c9da2 by Michael R. Crusoe at 2021-02-20T11:23:32+01:00
strip erroneous rpath
- - - - -
adb38f3c by Michael R. Crusoe at 2021-02-20T11:25:28+01:00
debian/rules: improve the clean target
- - - - -
736cca45 by Michael R. Crusoe at 2021-02-20T11:32:43+01:00
silence lintian false-positive
- - - - -
9e1fadef by Michael R. Crusoe at 2021-02-20T11:34:39+01:00
ready to upload lintian clean package
- - - - -
9 changed files:
- debian/changelog
- debian/control
- + debian/hyphy-common.lintian-overrides
- + debian/hyphy-mpi.lintian-overrides
- + debian/hyphy-pt.lintian-overrides
- debian/manuals/hyphy.1
- debian/patches/series
- + debian/patches/spelling
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+hyphy (2.5.28+dfsg-2) unstable; urgency=medium
+
+ * Team upload.
+ * debian/rules: set LC_ALL to fix groff warnings in the manpages
+ * debian/patches/spelling: fix some typos
+ * debian/rules: delete erroneous rpath for the MPI binaries
+ * debian/rules: improve the clean target
+
+ -- Michael R. Crusoe <crusoe at debian.org> Sat, 20 Feb 2021 10:57:19 +0100
+
hyphy (2.5.28+dfsg-1) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -11,7 +11,8 @@ Build-Depends: debhelper-compat (= 13),
libcurl4-gnutls-dev | libcurl4-dev,
libssl-dev,
libsqlite3-dev,
- pkg-config
+ pkg-config,
+ chrpath
Standards-Version: 4.5.1
Vcs-Browser: https://salsa.debian.org/med-team/hyphy
Vcs-Git: https://salsa.debian.org/med-team/hyphy.git
=====================================
debian/hyphy-common.lintian-overrides
=====================================
@@ -0,0 +1 @@
+hyphy-common: package-contains-documentation-outside-usr-share-doc usr/share/hyphy/TemplateBatchFiles/ProteinAnalyses/README_relative_prot_rates.md
=====================================
debian/hyphy-mpi.lintian-overrides
=====================================
@@ -0,0 +1 @@
+hyphy-mpi: typo-in-manual-page usr/share/man/man1/HYPHYMPI.1.gz gard guard
=====================================
debian/hyphy-pt.lintian-overrides
=====================================
@@ -0,0 +1 @@
+hyphy-pt: typo-in-manual-page usr/share/man/man1/hyphy.1.gz gard guard
=====================================
debian/manuals/hyphy.1
=====================================
@@ -217,7 +217,7 @@ prr
Using the model and the outgroup provided by the user, perform relative rate tests with all possible pair of species from the data file.
.TP
prrti
-Given a list of files (and optinally genetic code tables), perform relative ratio tests on all possible pair of the data files.
+Given a list of files (and optionally genetic code tables), perform relative ratio tests on all possible pair of the data files.
.TP
pdf
Read sequence data, select a contiguous subset of sites and save it to another datafile.
=====================================
debian/patches/series
=====================================
@@ -1,2 +1,3 @@
use_debian_sqlite.patch
rm_arch_specific_flags.patch
+spelling
=====================================
debian/patches/spelling
=====================================
@@ -0,0 +1,114 @@
+From: Michael R. Crusoe <crusoe at debian.org>
+Subject: fix typos
+Forwarded: https://github.com/veg/hyphy/pull/1289
+--- hyphy.orig/src/core/category.cpp
++++ hyphy/src/core/category.cpp
+@@ -177,7 +177,7 @@
+ !CheckEqual (iSplitter->GetMaxX(),1.0) ||
+ *theName == splitterName ||
+ (intervals = iSplitter->GetNumberOfIntervals()+1) < 2) {
+- HandleApplicationError (errorMsg & _String("Category variables which specify interval splitting options must be supported on [0,1], and not result in circular dependance"));
++ HandleApplicationError (errorMsg & _String("Category variables which specify interval splitting options must be supported on [0,1], and not result in circular dependence"));
+ return;
+ }
+
+@@ -475,7 +475,7 @@
+ }
+ }
+
+- // disallow category -> category dependance
++ // disallow category -> category dependence
+ for (long i=0; i<scannedVarsList.lLength; i++) {
+ _Variable * curVar = (_Variable*)variablePtrs (scannedVarsList.list_data[i]);
+ if (curVar->IsCategory()) {
+@@ -489,7 +489,7 @@
+ hiddenMarkovModel = HY_NO_MODEL;
+
+ parameterList.Duplicate (&scannedVarsList);
+- // finally go thru all the variables and put them where they belong in dependance containers
++ // finally go thru all the variables and put them where they belong in dependence containers
+
+ _SimpleList exclude;
+
+--- hyphy.orig/res/TemplateBatchFiles/files.lst
++++ hyphy/res/TemplateBatchFiles/files.lst
+@@ -108,4 +108,4 @@
+
+ "","Perform relative ratio tests.","!Relative Ratio";
+ "RRT","Use relative ratio test on 2 datasets and a variety of standard models","RelativeRatio.bf";
+-"PRRTI","Given a list of files (and optinally genetic code tables), perform relative ratio tests on all possible pair of the data files.","PairwiseRelativeRatio.bf";
++"PRRTI","Given a list of files (and optionally genetic code tables), perform relative ratio tests on all possible pair of the data files.","PairwiseRelativeRatio.bf";
+--- hyphy.orig/src/core/likefunc.cpp
++++ hyphy/src/core/likefunc.cpp
+@@ -2382,20 +2382,20 @@
+
+ //_______________________________________________________________________________________
+
+-void _LikelihoodFunction::RecurseConstantOnPartition (long blockIndex, long index, long dependance, long highestIndex, hyFloat weight, _Matrix& cache) {
++void _LikelihoodFunction::RecurseConstantOnPartition (long blockIndex, long index, long dependence, long highestIndex, hyFloat weight, _Matrix& cache) {
+ // SLKP 20210102: TODO this needs to be reviewed and confirmed as working.
+ _CategoryVariable* thisC = (_CategoryVariable*)LocateVar(indexCat.list_data[index]);
+
+ if (index<highestIndex) {
+- if ((!CheckNthBit(dependance,index))||thisC->is_hidden_markov()) {
+- RecurseCategory (blockIndex, index+1, dependance,highestIndex,weight);
++ if ((!CheckNthBit(dependence,index))||thisC->is_hidden_markov()) {
++ RecurseCategory (blockIndex, index+1, dependence,highestIndex,weight);
+ } else {
+ thisC->Refresh();
+ long nI = thisC->GetNumberOfIntervals ();
+ offsetCounter *= nI;
+ for (long k = 0; k<nI; k++) {
+ thisC->SetIntervalValue(k);
+- RecurseConstantOnPartition(blockIndex,index+1,dependance, highestIndex,weight*thisC->GetIntervalWeight(k),cache);
++ RecurseConstantOnPartition(blockIndex,index+1,dependence, highestIndex,weight*thisC->GetIntervalWeight(k),cache);
+ categID+=offsetCounter/nI;
+ }
+ offsetCounter/=nI;
+@@ -2450,7 +2450,7 @@
+
+ //_______________________________________________________________________________________
+
+-void _LikelihoodFunction::RecurseCategory(long blockIndex, long index, long dependance, long highestIndex, hyFloat weight
++void _LikelihoodFunction::RecurseCategory(long blockIndex, long index, long dependence, long highestIndex, hyFloat weight
+ #ifdef _SLKP_LFENGINE_REWRITE_
+ ,_SimpleList* siteMultipliers, char runMode, hyFloat *runStorage,
+ long branchIndex, _SimpleList* branchValues
+@@ -2459,8 +2459,8 @@
+ {
+ _CategoryVariable* thisC = (_CategoryVariable*)LocateVar(indexCat.list_data[index]);
+ if (index<highestIndex) {
+- if ((!CheckNthBit(dependance,index))||thisC->is_hidden_markov())
+- RecurseCategory (blockIndex, index+1, dependance,highestIndex,weight
++ if ((!CheckNthBit(dependence,index))||thisC->is_hidden_markov())
++ RecurseCategory (blockIndex, index+1, dependence,highestIndex,weight
+ #ifdef _SLKP_LFENGINE_REWRITE_
+ ,siteMultipliers,runMode,runStorage
+ #endif
+@@ -2471,7 +2471,7 @@
+ offsetCounter *= nI;
+ for (long k = 0; k<nI; k++) {
+ thisC->SetIntervalValue(k);
+- RecurseCategory(blockIndex,index+1,dependance, highestIndex,weight*thisC->GetIntervalWeight(k)
++ RecurseCategory(blockIndex,index+1,dependence, highestIndex,weight*thisC->GetIntervalWeight(k)
+ #ifdef _SLKP_LFENGINE_REWRITE_
+ ,siteMultipliers,runMode,runStorage,branchIndex,branchValues
+ #endif
+@@ -2698,7 +2698,7 @@
+ {
+ _Matrix dependancies (MAX(3,indexDep.lLength),indexInd.lLength,true,true);
+
+- // element (i,j) represents the dependance of i-th dep var on the j-th ind var
++ // element (i,j) represents the dependence of i-th dep var on the j-th ind var
+ // 0 - no dep,
+ // 1 -> monotone increase,
+ // -1 -> monotone decrease
+@@ -7678,7 +7678,7 @@
+
+ avl.ReorderList();
+
+- if (templateKind<0) { // remove dependance of the function from the HMM model specifier
++ if (templateKind<0) { // remove dependence of the function from the HMM model specifier
+ allVariables.Delete (allVariables.Find(-templateKind-1));
+ rankVariables.Delete ((BaseRef)(-templateKind-1));
+ }
=====================================
debian/rules
=====================================
@@ -3,6 +3,7 @@
# DH_VERBOSE := 1
export DEB_BUILD_MAINT_OPTIONS = hardening=+bindnow
+export LC_ALL=C.UTF-8
include /usr/share/dpkg/default.mk
@@ -15,6 +16,10 @@ ISOFILES += res/TemplateBatchFiles/TemplateModels/models.lst
dh $@ --buildsystem=cmake
override_dh_auto_clean:
+ifeq (amd64,$(DEB_HOST_ARCH))
+ dh_auto_clean --builddirectory obj-avx
+ dh_auto_clean --builddirectory obj-sse3
+endif
dh_auto_clean
override_dh_auto_configure:
@@ -43,6 +48,7 @@ endif
override_dh_install-arch:
dh_install -a
+ chrpath --delete obj-*/HYPHYMPI
ifeq (amd64,$(DEB_HOST_ARCH))
mkdir -p debian/hyphy-mpi/usr/lib/$(DEB_SOURCE)/bin
mkdir -p debian/hyphy-pt/usr/lib/$(DEB_SOURCE)/bin
View it on GitLab: https://salsa.debian.org/med-team/hyphy/-/compare/4682e91cbed5f0ba25d744916f58ec8678c5bb81...9e1fadefc4b130ecff00222b42b7a10d02dafea7
--
View it on GitLab: https://salsa.debian.org/med-team/hyphy/-/compare/4682e91cbed5f0ba25d744916f58ec8678c5bb81...9e1fadefc4b130ecff00222b42b7a10d02dafea7
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